(We surveyed bacterial and archaeal diversity using amplicon sequencing of the 16S rRNA gene, a common taxonomic marker for bacteria and archaea12 that remains a valuable tool for microbial ecology despite the introduction of whole-genome methods (e.g., metagenomics) that capture gene-level function...
This study investigated the microbiology in the boning room of an integrated (abattoir A) and a fragmented (abattoir B) Australian beef export abattoirs using culture independent 16S rRNA gene amplicon sequencing coupled with total viable count (TVC). Transmission of microbial populations during ...
16S and ITS rRNA sequencing are culture-free methods to identify and compare bacterial diversity from complex microbiomes or environments that are difficult to study.
Pichler M, Coskun ÖK, Ortega-Arbulú AS, Conci N, Wörheide G, Vargas S, Orsi WD. A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform. Microbiologyopen. 2018 Dec;7(6):e00611. Yeo K, Connell J, Bouras G, Smith E, Murphy W, Hodge JC, Krishnan S,...
Figure 1: Amplicon sequencing of 16s rDNA gene. (A) Schematic workflow to examine the composition of the mouse gut microbiota using the nanopore (MinION) and the short-read (Illumina MiSeq) sequencing. (B) The distribution of PHRED quality scores of short-read sequencing data and pass 2D re...
protocol described elsewhere37. A dual-indexing amplification and sequencing approach was used and the resulting amplicons were purified and subjected to paired-end sequencing (2 × 250 bp) of one pooled amplicon sample on two runs of the Illumina MiSeq platform, one for broilers and ...
还发现和之前的处理过程类似的一个流程,意大利面。adlape95/Spaghetti: Spaghetti: in situ analysis of 16S rRNA amplicons obtained by nanopore sequencing (github.com) Spaghetti 是用于纳米孔测序数据的自动生物信息学分析以及半自动探索性分析和数据可视化的定制管道。该管道专为原位分析MinION(牛津纳米孔技术公司,...
Zhang W, Fan X, Shi H, Li J, Zhang M, Zhao J, Su X. Comprehensive Assessment of 16S rRNA Gene Amplicon Sequencing for Microbiome Profiling across Multiple Habitats. Microbiol Spectr. 2023 Jun 15;11(3):e0056323. Bel Mokhtar N, Catalá-Oltra M, Stathopoulou P, Asimakis E, Remmal I...
In the first step of our analysis, we used the large set of template and complement reads to assess the global performance of the amplicon sequencing process. Consequently, we analysed basic read-mapping statistics to uncover potential pitfalls of the MinION platform and tried to reconstruct the ...
A similar protocol was employed to process arctic sediment samples to characterize bacterial community structure by 16S rRNA amplicon sequencing [17]. However, there is no comprehensive information on sequential membrane filtration's potential biases on the retained microbial taxa than its non-processed ...